Abstract: Systems and methods for predicting protein-ligand interactions are disclosed. An exemplary method can include identifying a set of structural neighbours of the query proteins, where each of contains ligands. The method can also determine a similarity score for each of the structural neighbours representing configuration similarity and interaction tendency between the structural neighbours and predict protein-ligand interactions of the one or more query proteins using the similarity scores.

Abstract: The present subject matter relates to systems and methods for predicting molecular interactions within biological networks based on structural and non-structural indicators. Such molecules include but are not limited to proteins, nucleic acids and small molecules. In some embodiments, the present subject matter is directed to methods for predicting protein-protein interactions comprising obtaining a pair of query proteins, using sequence alignment to identify structural representatives for each of the pair of query proteins, and using structural alignment to determine sets of close and remote structural neighbors for each of the structural representatives. The method can include analyzing the close and remote structural neighbors to identify a reported complex, and using the reported complex to define a template for creating a model for interaction of the pair of query proteins.

Abstract: A process for determination of three-dimensional macromolecular atomic structures of proteins is provided. A plurality of gene products are clustered into at least one family of homologous sequences. At least one protein encoded by a sequence selected from each of the families is prepared, purified and characterized. The purified proteins are crystallized in parallel against crystallization screens. Diffraction data produced by the crystallized proteins is measured using a multi-wavelength anomalous diffraction method. The diffraction data is analyzed by using a multi-wavelength anomalous diffraction phasing method, an atomic model is built, and the model is refined based on the diffraction data to determine a three-dimensional macromolecular atomic structure for each of the crystallized proteins.

Abstract: A process for pan-genomic determination of three-dimensional macromolecular atomic structures uses a unique combination of components. All known structural information, sequence information and functional information are systematically organized into a genomics database. Advanced tools of bioinformatics are used to cluster all known gene products into families of homologous sequences. Simultaneously, in parallel for each such family, a few cDNAs from appropriately representatives species are cloned into expression vectors for a few expressions systems. Constructs are then screened for expression, and those that are effective advance to the preparative step. Expressed proteins are prepared, purified and characterized. Purified proteins are set to crystallize in parallel against crystallization screens. Crystals that grow are tested for suitable diffraction characteristics.

Abstract: A process pan-genomic determination of three-dimensional macromolecular atomic structures uses a unique combination of components.